Cobalt in PDB 4fen: Crystal Structure of the A24U/U25A/A46G Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine

The structure of Crystal Structure of the A24U/U25A/A46G Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine, PDB code: 4fen was solved by C.D.Stoddard, J.J.Trausch, J.Widmann, J.Marcano, R.Knight, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	133.689, 35.347, 41.388, 90.00, 91.39, 90.00
R / Rfree (%)	16.4 / 19.1

The binding sites of Cobalt atom in the Crystal Structure of the A24U/U25A/A46G Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine (pdb code 4fen). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 7 binding sites of Cobalt where determined in the Crystal Structure of the A24U/U25A/A46G Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine, PDB code: 4fen:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7;

Cobalt binding site 1 out of 7 in the Crystal Structure of the A24U/U25A/A46G Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of the A24U/U25A/A46G Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co103 b:8.0 occ:1.00 CO B:NCO103 0.0 8.0 1.0 N6 B:NCO103 2.0 10.4 1.0 N4 B:NCO103 2.0 9.8 1.0 N1 B:NCO103 2.0 10.5 1.0 N5 B:NCO103 2.0 9.0 1.0 N3 B:NCO103 2.0 9.1 1.0 N2 B:NCO103 2.0 11.1 1.0 O B:HOH534 3.8 20.9 1.0 O B:HOH462 3.9 18.0 1.0 O B:HOH323 3.9 8.8 1.0 O B:HOH320 3.9 12.9 1.0 O B:HOH349 4.0 13.0 1.0 OP1 B:U67 4.1 6.9 1.0 O B:HOH503 4.2 23.5 1.0 O3' B:A66 4.4 6.5 1.0 O B:HOH331 4.5 11.6 1.0 P B:U67 4.9 5.3 1.0 O2' B:A66 5.0 7.5 1.0

Cobalt binding site 2 out of 7 in the Crystal Structure of the A24U/U25A/A46G Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of the A24U/U25A/A46G Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co104 b:9.3 occ:1.00 CO B:NCO104 0.0 9.3 1.0 N3 B:NCO104 2.0 11.9 1.0 N6 B:NCO104 2.0 11.4 1.0 N4 B:NCO104 2.0 15.0 1.0 N5 B:NCO104 2.0 11.2 1.0 N1 B:NCO104 2.0 11.4 1.0 N2 B:NCO104 2.0 13.8 1.0 O B:HOH621 3.8 57.0 1.0 O B:HOH386 3.9 14.6 1.0 O B:HOH434 3.9 24.2 1.0 O4 B:U69 4.0 6.9 1.0 O B:HOH444 4.1 21.3 1.0 O6 B:G56 4.1 7.7 1.0 O B:HOH391 4.1 14.0 1.0 O B:HOH306 4.3 10.9 1.0 O B:HOH437 4.4 20.5 1.0 OP2 B:C39 4.4 9.8 1.0 O B:HOH535 4.5 29.6 1.0 OP1 B:C39 4.6 10.3 1.0 N7 B:G56 4.6 6.6 1.0 O6 B:G68 4.7 6.8 1.0 C6 B:G56 5.0 6.6 1.0

Cobalt binding site 3 out of 7 in the Crystal Structure of the A24U/U25A/A46G Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of the A24U/U25A/A46G Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co105 b:26.2 occ:1.00 CO B:NCO105 0.0 26.2 1.0 N3 B:NCO105 2.0 25.8 1.0 N4 B:NCO105 2.0 26.1 1.0 N2 B:NCO105 2.0 25.6 1.0 N5 B:NCO105 2.0 25.9 1.0 N6 B:NCO105 2.0 25.4 1.0 N1 B:NCO105 2.0 26.2 1.0 O B:HOH786 3.6 41.4 1.0 O B:HOH400 3.7 16.5 1.0 O B:HOH595 3.8 26.1 1.0 O B:HOH511 3.8 17.0 1.0 OP1 B:G38 3.8 7.1 1.0 O B:HOH715 3.8 33.5 1.0 OP1 B:G56 4.0 14.4 1.0 O B:HOH500 4.0 26.8 1.0 O B:HOH797 4.3 0.0 1.0 OP2 B:G56 4.8 14.2 1.0 P B:G38 4.9 6.3 1.0 OP2 B:G38 4.9 8.6 1.0 O B:HOH570 4.9 21.1 1.0 O B:HOH428 4.9 25.9 1.0 P B:G56 5.0 12.8 1.0

Cobalt binding site 4 out of 7 in the Crystal Structure of the A24U/U25A/A46G Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of the A24U/U25A/A46G Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co106 b:6.0 occ:1.00 CO B:NCO106 0.0 6.0 1.0 N5 B:NCO106 2.0 7.3 1.0 N2 B:NCO106 2.0 7.8 1.0 N1 B:NCO106 2.0 7.4 1.0 N6 B:NCO106 2.0 7.4 1.0 N3 B:NCO106 2.0 7.9 1.0 N4 B:NCO106 2.0 6.4 1.0 O B:HOH316 3.6 37.5 1.0 OP2 B:A66 3.9 9.3 1.0 O B:HOH307 3.9 10.4 1.0 O6 B:G32 4.0 6.1 1.0 O6 B:G31 4.1 5.8 1.0 O B:HOH357 4.1 12.3 1.0 O B:HOH327 4.2 9.5 1.0 O B:HOH318 4.2 8.9 1.0 O B:HOH415 4.2 20.3 1.0 O B:HOH340 4.2 10.9 1.0 O B:HOH309 4.3 9.8 1.0 N7 B:G31 4.4 5.2 1.0 C6 B:G31 4.9 5.7 1.0 O B:HOH708 4.9 27.1 1.0 O4 B:U30 5.0 6.5 1.0 C6 B:G32 5.0 5.7 1.0 O B:HOH302 5.0 7.2 1.0 C5 B:G31 5.0 5.7 1.0

Cobalt binding site 5 out of 7 in the Crystal Structure of the A24U/U25A/A46G Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of the A24U/U25A/A46G Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co107 b:25.4 occ:1.00 CO B:NCO107 0.0 25.4 1.0 N6 B:NCO107 2.0 26.7 1.0 N4 B:NCO107 2.0 26.3 1.0 N1 B:NCO107 2.0 26.6 1.0 N5 B:NCO107 2.0 27.0 1.0 N2 B:NCO107 2.0 26.0 1.0 N3 B:NCO107 2.0 25.4 1.0 O B:HOH637 3.7 40.5 1.0 O B:HOH695 3.7 20.0 1.0 O B:HOH479 3.7 21.7 1.0 OP2 B:G37 4.0 7.7 1.0 O B:HOH378 4.1 15.3 1.0 O B:HOH547 4.1 29.1 1.0 O6 B:G38 4.2 6.7 1.0 N7 B:G38 4.2 6.7 1.0 O B:HOH864 4.3 0.5 1.0 O B:HOH477 4.5 18.8 1.0 N7 B:G37 4.5 6.4 1.0 O B:HOH719 4.5 27.4 1.0 C6 B:G38 4.9 6.9 1.0 C5 B:G38 4.9 4.9 1.0 O B:HOH509 4.9 22.7 1.0

Cobalt binding site 6 out of 7 in the Crystal Structure of the A24U/U25A/A46G Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure of the A24U/U25A/A46G Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co108 b:15.7 occ:1.00 CO B:NCO108 0.0 15.7 1.0 N3 B:NCO108 2.0 17.3 1.0 N5 B:NCO108 2.0 18.5 1.0 N1 B:NCO108 2.0 17.2 1.0 N2 B:NCO108 2.0 18.8 1.0 N6 B:NCO108 2.0 17.6 1.0 N4 B:NCO108 2.0 17.9 1.0 O B:HOH673 3.8 24.9 1.0 O B:HOH504 4.1 25.6 1.0 O6 B:G46 4.2 9.1 1.0 O B:HOH379 4.3 15.1 1.0 O4 B:U47 4.3 12.6 1.0 O B:HOH634 4.3 26.0 1.0 O B:HOH537 4.3 20.7 1.0 N7 B:G46 4.3 9.2 1.0 O B:HOH429 4.4 25.0 1.0 O B:HOH672 4.7 25.4 1.0 O B:HOH480 4.8 23.7 1.0 O B:HOH538 4.9 23.2 1.0 C6 B:G46 5.0 9.6 1.0

Cobalt binding site 7 out of 7 in the Crystal Structure of the A24U/U25A/A46G Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Crystal Structure of the A24U/U25A/A46G Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co109 b:10.1 occ:0.64 CO B:NCO109 0.0 10.1 0.6 N1 B:NCO109 2.0 12.3 0.6 N6 B:NCO109 2.0 11.3 0.6 N3 B:NCO109 2.0 10.7 0.6 N4 B:NCO109 2.0 9.5 0.6 N5 B:NCO109 2.0 11.4 0.6 N2 B:NCO109 2.0 10.7 0.6 O B:HOH820 4.0 43.8 1.0 O B:HOH685 4.1 22.9 1.0 OP1 B:G72 4.1 7.4 1.0 OP1 B:A73 4.1 12.9 1.0 O B:HOH760 4.2 38.1 1.0 O B:HOH777 4.2 41.2 1.0 O B:HOH330 4.2 13.2 1.0 O B:HOH533 4.3 19.0 1.0 O B:HOH560 4.4 35.5 1.0 OP2 B:A73 4.9 12.5 1.0

C.D.Stoddard, J.Widmann, J.J.Trausch, J.G.Marcano-Velazquez, R.Knight, R.T.Batey. Nucleotides Adjacent to the Ligand-Binding Pocket Are Linked to Activity Tuning in the Purine Riboswitch. J.Mol.Biol. V. 425 1596 2013.
ISSN: ISSN 0022-2836
PubMed: 23485418
DOI: 10.1016/J.JMB.2013.02.023